Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F2 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,961,177 |
C→G |
A40P (GCC→CCC) |
cheZ ← |
protein phosphatase CheZ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,961,177 | 0 | C | G | 76.2%
| 40.8
/ 11.4
| 21 | A40P (GCC→CCC) | cheZ | protein phosphatase CheZ |
| Reads supporting (aligned to +/- strand): ref base C (3/2); new base G (9/7); total (12/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAA > NZ_CP009273/1961117‑1961242
|
gCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGt < 2:691717/90‑1 (MQ=255)
acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc < 1:485026/90‑1 (MQ=255)
acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc < 1:488997/90‑1 (MQ=255)
acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc < 2:149267/90‑1 (MQ=255)
acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc < 2:467967/90‑1 (MQ=255)
acaTAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc > 2:164121/1‑90 (MQ=255)
tAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCgcagc > 1:97031/1‑90 (MQ=255)
tACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATa < 1:597551/90‑1 (MQ=255)
tACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCTCGCAGCATa < 2:228949/90‑1 (MQ=255)
gaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg > 2:20599/2‑90 (MQ=255)
aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg > 1:106346/1‑90 (MQ=255)
aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg > 2:68326/1‑90 (MQ=255)
aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg > 2:367493/1‑90 (MQ=255)
aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcgcg > 2:664537/1‑90 (MQ=255)
aaCGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTAGCGCAGCATAcgcg > 1:83368/1‑90 (MQ=255)
cGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc < 1:452332/78‑1 (MQ=255)
cGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCgcgc > 2:452332/1‑78 (MQ=255)
tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg > 2:353806/1‑90 (MQ=255)
tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg > 2:686771/1‑90 (MQ=255)
tCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAgg > 2:771679/1‑90 (MQ=255)
tGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCaa < 1:622698/90‑1 (MQ=255)
|
GCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAA > NZ_CP009273/1961117‑1961242
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACTGTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAGCAGGT > NZ_CP009273/1961079‑1961274
|
ACTGTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGC < SRR3722079.521692/100‑1 (MQ=60)
ctggtctcgtgggctcggagatgtgtataagagacagACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCC < SRR3722079.752246/63‑1 (MQ=60)
CTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGC > SRR3722079.97798/1‑100 (MQ=60)
AGATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCG < SRR3722079.456293/100‑1 (MQ=60)
ACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCctgtctcttatacacatctccgagcccacgagaccag > SRR3722079.45932/1‑63 (MQ=60)
ACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCG > SRR3722079.107214/1‑100 (MQ=60)
ACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCG < SRR3722079.489257/100‑1 (MQ=60)
ACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCG < SRR3722079.493297/100‑1 (MQ=60)
ACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTAGCGCAGCATACGCG > SRR3722079.84040/1‑100 (MQ=60)
TACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGC < SRR3722079.603548/100‑1 (MQ=60)
TGGCTTCCGCCGCTTCGGCAATGGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCC < SRR3722079.629035/100‑1 (MQ=60)
GGGCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAGCAGGT > SRR3722079.428974/1‑100 (MQ=60)
GGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAGCAGGT > SRR3722079.564585/1‑100 (MQ=60)
|
ACTGTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCGTCAGCAGGT > NZ_CP009273/1961079‑1961274
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
